[gmx-users] Error while running protein-carbohydrate simulation
Deep Bhattacharya
deep.bhattacharya1991 at gmail.com
Mon Jul 11 01:21:35 CEST 2016
Evan,
One more question,
Do I also increase the equilibration time from 100ps to 200ps? Will that help along with the 1fs time step?
Sincerely,
Deep
Sent from my iPhone
> On Jul 10, 2016, at 6:09 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
>
> I usually set tau-t=2.0 and tau-p=6.0 for most of my bulk fluid systems.
> It really depends on what you are simulating so just be sure to check the
> temperature and pressure to ensure that they are remaining constant and
> within your desired tolerances.
>
> I think you may have to change your pressure algorithm to Berendsen if you
> are using the Nose-Hoover thermostat, but definitely read about that in the
> gromacs manual. Nose-Hoover usually produces an accurate thermodynamic
> ensemble which is valuable if you are doing anything with energies.
>
> Evan L.
> On Jul 10, 2016 5:00 PM, "Deep Bhattacharya" <hypergenetics at gmail.com>
> wrote:
>
>> Thank you Evan for your response.
>> What time would you suggest for the coupling time for temperature and
>> pressure? Yes I will use the Nose-Hoover thermostat and see how the
>> simulation goes.
>> So you mean to change like this
>>
>>
>> ; Temperature coupling =
>>
>> tcoupl = nose-hoover
>>
>> ; Groups to couple separately =
>>
>> tc-grps = PROTEIN SOL_Na
>>
>> ; Time constant (ps) and reference temperature (K) =
>>
>> tau-t = 0.5 0.5
>>
>> ref-t = 300 300
>>
>> ; Pressure coupling =
>>
>> Pcoupl = parrinello-rahman
>>
>> Pcoupltype = isotropic
>>
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
>>
>> tau-p = 5.0
>>
>> compressibility = 4.5E-5
>>
>> ref-p = 1.0
>>
>> Awaiting your response
>> Thank you.
>>
>>
>> Deep
>>
>>> On Sun, Jul 10, 2016 at 5:53 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
>>>
>>> Try running with a 1 fs time step in stead of 2 fs. Also view your
>>> trajectory to see if anything is messed up. Try re-minimizing as well. If
>>> that doesn't work, you could change the coupling time for the temperature
>>> and pressure.
>>>
>>> On another note, why not use the Nose-Hoover thermostat? It may be more
>>> accurate for the energies in your system.
>>>
>>> Best of luck,
>>>
>>> Evan L.
>>> On Jul 10, 2016 4:45 PM, "Deep Bhattacharya" <hypergenetics at gmail.com>
>>> wrote:
>>>
>>>> Hello,
>>>> I am trying to simulate the system mentioned but its failing showing
>> this
>>>> error message,
>>>> WARNING: Listed nonbonded interaction between particles 746 and 751
>>>> at distance 3f which is larger than the table limit 3f nm.
>>>>
>>>> This is likely either a 1,4 interaction, or a listed interaction inside
>>>> a smaller molecule you are decoupling during a free energy calculation.
>>>> Since interactions at distances beyond the table cannot be computed,
>>>> they are skipped until they are inside the table limit again. You will
>>>> only see this message once, even if it occurs for several interactions.
>>>>
>>>> IMPORTANT: This should not happen in a stable simulation, so there is
>>>> probably something wrong with your system. Only change the
>>> table-extension
>>>> distance in the mdp file if you are really sure that is the reason.
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> Program mdrun, VERSION 4.6.5
>>>> Source code file: /util/src/gromacs/gromacs-4.6.5/src/mdlib/pme.c,
>> line:
>>>> 851
>>>>
>>>> Fatal error:
>>>> 1 particles communicated to PME node 13 are more than 2/3 times the
>>> cut-off
>>>> out of the domain decomposition cell of their charge group in dimension
>>> y.
>>>> This usually means that your system is not well equilibrated.
>>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>> -------------------------------------------------------
>>>>
>>>> "Jede der Scherben spiegelt das Licht" (Wir sind Helden)
>>>>
>>>> Error on node 13, will try to stop all the nodes
>>>> Halting parallel program mdrun on CPU 13 out of 16
>>>>
>>>> gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden)
>> --------------------------------------------------------------------------
>>>> MPI_ABORT was invoked on rank 13 in communicator MPI_COMM_WORLD
>>>> with errorcode -1.
>>>>
>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>> You may or may not see output from other processes, depending on
>>>> exactly when Open MPI kills them.
>> --------------------------------------------------------------------------
>> --------------------------------------------------------------------------
>>>> mpirun has exited due to process rank 13 with PID 117399 on
>>>> node c0323 exiting improperly. There are two reasons this could occur:
>>>>
>>>> 1. this process did not call "init" before exiting, but others in
>>>> the job did. This can cause a job to hang indefinitely while it waits
>>>> for all processes to call "init". By rule, if one process calls "init",
>>>> then ALL processes must call "init" prior to termination.
>>>>
>>>> 2. this process called "init", but exited without calling "finalize".
>>>> By rule, all processes that call "init" MUST call "finalize" prior to
>>>> exiting or it will be considered an "abnormal termination"
>>>>
>>>> This may have caused other processes in the application to be
>>>> terminated by signals sent by mpirun (as reported here).
>> --------------------------------------------------------------------------
>>>>
>>>> Here is my .mdp file
>>>> title = CD44 deHA_sulf_red complex MD simulation
>>>> ; Run parameters
>>>> integrator = md ; leap-frog integrator
>>>> nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
>>>> dt = 0.002 ; 2 fs
>>>> ; Output control
>>>> nstxout = 50000 ; suppress .trr output
>>>> nstvout = 50000 ; suppress .trr output
>>>> nstenergy = 50000 ; save energies every 100.0 ps
>>>> nstlog = 50000 ; update log file every 100.0 ps
>>>> compressed-x-grps = System
>>>> energygrps = Protein LIG
>>>> ; Bond parameters
>>>> continuation = yes ; first dynamics run
>>>> constraint_algorithm = lincs ; holonomic constraints
>>>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>>>> constrained
>>>> lincs_iter = 1 ; accuracy of LINCS
>>>> lincs_order = 4 ; also related to accuracy
>>>> ; Neighborsearching
>>>> cutoff-scheme = Verlet
>>>> ns_type = grid ; search neighboring grid cells
>>>> nstlist = 10 ; 20 fs, largely irrelevant with Verlet
>>>> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
>>>> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
>>>> ; Electrostatics
>>>> coulombtype = PME ; Particle Mesh Ewald for long-range
>>>> electrostatics
>>>> pme_order = 4 ; cubic interpolation
>>>> fourierspacing = 0.16 ; grid spacing for FFT
>>>> ; Temperature coupling
>>>> tcoupl = V-rescale ; modified Berendsen
>>> thermostat
>>>> tc-grps = Protein_LIG Water_and_ions ; two coupling groups -
>> more
>>>> accurate
>>>> tau_t = 0.1 0.1 ; time constant, in ps
>>>> ref_t = 300 300 ; reference temperature,
>> one
>>>> for each group, in K
>>>> ; Pressure coupling
>>>> pcoupl = Parrinello-Rahman ; pressure coupling is on
>> for
>>>> NPT
>>>> pcoupltype = isotropic ; uniform scaling of box
>>>> vectors
>>>> tau_p = 2.0 ; time constant, in ps
>>>> ref_p = 1.0 ; reference pressure, in
>> bar
>>>> compressibility = 4.5e-5 ; isothermal
>> compressibility
>>> of
>>>> water, bar^-1
>>>> ; Periodic boundary conditions
>>>> pbc = xyz ; 3-D PBC
>>>> ; Dispersion correction
>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>> ; Velocity generation
>>>> gen_vel = no ; assign velocities from Maxwell distribution
>>>>
>>>> I have performed 100 ps NVT and NPT simulation before doing the MD run.
>>>> Please help
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *Deep S Bhattacharya*
>>>>
>>>> *Graduate Research Assistant*
>>>>
>>>> Mohs Biomedical Imaging & Nanotechnology Group
>>>>
>>>> Pharmaceutical Sciences
>>>>
>>>> *University of Nebraska Medical Center*
>>>>
>>>> 4018 Eppley Science Hall | Omaha, NE 68198-6805
>>>>
>>>> office 402.559.4349 | cell 402.906.1640
>>>>
>>>> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
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>>
>>
>>
>> --
>> Deep Bhattacharya.
>> Post-Graduate Student,
>> Department of Pharmaceutical Chemistry,
>> Bombay College Of Pharmacy.
>> Mobile - +918976129616
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